Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.

Resolving the role of natural selection is a basic objective of evolutionary biology. It is generally difficult to detect the influence of selection because ubiquitous non-selective stochastic change in allele frequencies (genetic drift) degrades evidence of selection. As a result, selection scans t...

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Autor principal:	Jason Bertram
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Genetics QH426-470
Acceso en línea:	https://doaj.org/article/9ac76b2e32b9453fba07862a95634425
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spelling	oai:doaj.org-article:9ac76b2e32b9453fba07862a956344252021-12-02T20:03:01ZAllele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.1553-73901553-740410.1371/journal.pgen.1009833https://doaj.org/article/9ac76b2e32b9453fba07862a956344252021-09-01T00:00:00Zhttps://doi.org/10.1371/journal.pgen.1009833https://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Resolving the role of natural selection is a basic objective of evolutionary biology. It is generally difficult to detect the influence of selection because ubiquitous non-selective stochastic change in allele frequencies (genetic drift) degrades evidence of selection. As a result, selection scans typically only identify genomic regions that have undergone episodes of intense selection. Yet it seems likely such episodes are the exception; the norm is more likely to involve subtle, concurrent selective changes at a large number of loci. We develop a new theoretical approach that uncovers a previously undocumented genome-wide signature of selection in the collective divergence of allele frequencies over time. Applying our approach to temporally resolved allele frequency measurements from laboratory and wild Drosophila populations, we quantify the selective contribution to allele frequency divergence and find that selection has substantial effects on much of the genome. We further quantify the magnitude of the total selection coefficient (a measure of the combined effects of direct and linked selection) at a typical polymorphic locus, and find this to be large (of order 1%) even though most mutations are not directly under selection. We find that selective allele frequency divergence is substantially elevated at intermediate allele frequencies, which we argue is most parsimoniously explained by positive-not negative-selection. Thus, in these populations most mutations are far from evolving neutrally in the short term (tens of generations), including mutations with neutral fitness effects, and the result cannot be explained simply as an ongoing purging of deleterious mutations.Jason BertramPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 9, p e1009833 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Genetics QH426-470
spellingShingle	Genetics QH426-470 Jason Bertram Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.
description	Resolving the role of natural selection is a basic objective of evolutionary biology. It is generally difficult to detect the influence of selection because ubiquitous non-selective stochastic change in allele frequencies (genetic drift) degrades evidence of selection. As a result, selection scans typically only identify genomic regions that have undergone episodes of intense selection. Yet it seems likely such episodes are the exception; the norm is more likely to involve subtle, concurrent selective changes at a large number of loci. We develop a new theoretical approach that uncovers a previously undocumented genome-wide signature of selection in the collective divergence of allele frequencies over time. Applying our approach to temporally resolved allele frequency measurements from laboratory and wild Drosophila populations, we quantify the selective contribution to allele frequency divergence and find that selection has substantial effects on much of the genome. We further quantify the magnitude of the total selection coefficient (a measure of the combined effects of direct and linked selection) at a typical polymorphic locus, and find this to be large (of order 1%) even though most mutations are not directly under selection. We find that selective allele frequency divergence is substantially elevated at intermediate allele frequencies, which we argue is most parsimoniously explained by positive-not negative-selection. Thus, in these populations most mutations are far from evolving neutrally in the short term (tens of generations), including mutations with neutral fitness effects, and the result cannot be explained simply as an ongoing purging of deleterious mutations.
format	article
author	Jason Bertram
author_facet	Jason Bertram
author_sort	Jason Bertram
title	Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.
title_short	Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.
title_full	Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.
title_fullStr	Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.
title_full_unstemmed	Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.
title_sort	allele frequency divergence reveals ubiquitous influence of positive selection in drosophila.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/9ac76b2e32b9453fba07862a95634425
work_keys_str_mv	AT jasonbertram allelefrequencydivergencerevealsubiquitousinfluenceofpositiveselectionindrosophila
_version_	1718375674766426112

Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.

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